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Xiao Y, Tan M, Song J, Huang Y, Lv M, Liao M, Yu Z, Gao Z, Qu S, Liang W. Developmental validation of an mRNA kit: A 5-dye multiplex assay designed for body-fluid identification. Forensic Sci Int Genet 2024; 71:103045. [PMID: 38615496 DOI: 10.1016/j.fsigen.2024.103045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024]
Abstract
Identifying the sources of biosamples found at crime scenes is crucial for forensic investigations. Among the markers used for body fluid identification (BFI), mRNA has emerged as a well-studied marker because of its high specificity and remarkable stability. Despite this potential, commercially available mRNA kits specifically designed for BFI are lacking. Therefore, we developed an mRNA kit that includes 21 specific mRNA markers of body fluids, along with three housekeeping genes for BFI, to identify four forensic-relevant fluids (blood, semen, saliva, and vaginal fluids). In this study, we tested 451 single-body-fluid samples, validated the universality of the mRNA kit, and obtained a gene expression profile. We performed the validation studies in triplicates and determined the sensitivity, specificity, stability, precision, and repeatability of the mRNA kit. The sensitivity of the kit was found to be 0.1 ng. Our validation process involved the examination of 59 RNA mixtures, 60 body fluids mixtures, and 20 casework samples, which further established the reliability of the kit. Furthermore, we constructed five classifiers that can handle single-body fluids and mixtures using this kit. The classifiers output possibility values and identify the specific body fluids of interest. Our results showed the reliability and suitability of the BFI kit, and the Random Forest classifier performed the best, with 94% precision. In conclusion, we developed an mRNA kit for BFI which can be a promising tool for forensic practice.
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Affiliation(s)
- Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jinlong Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yihang Huang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Zailiang Yu
- Suzhou Microread Genetics Co.,Ltd, Suzhou, Jiangsu, PR China
| | - Zhixiao Gao
- Suzhou Microread Genetics Co.,Ltd, Suzhou, Jiangsu, PR China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China.
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, PR China.
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2
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Kubo S, Amai K, Tanaka J, Niimi H. One-tube, two-step isothermal amplification of histatin 3 mRNA for saliva screening. Forensic Sci Int 2023; 352:111847. [PMID: 37837846 DOI: 10.1016/j.forsciint.2023.111847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/23/2023] [Indexed: 10/16/2023]
Abstract
Saliva samples are frequently collected at crime scenes. Salivary mRNA profiling, such as that of histatin 3 (HTN3), is a highly specific approach that overcomes the limitation of traditional amylase tests. However, typical mRNA detection methods based on reverse transcription PCR (RT-PCR) are time-consuming and labor-intensive. Here, we report a one-tube, two-step isothermal amplification assay for HTN3 mRNA, which enables rapid, simple, and sensitive screening of saliva. The first step is an RT-recombinase polymerase amplification (RT-RPA) assay at 42 °C for 20 min; the second step is a loop-mediated isothermal amplification (LAMP) assay at 65 °C for 30 min. The reactions can be performed in a closed tube, and the products are detected using real-time fluorescence analysis. The assay sensitivity was 0.5 µL of saliva samples. It also detected HTN3 mRNA in mixed and mock samples, demonstrating its applicability to actual forensic samples. These findings suggest that our strategy is promising for screening of saliva from forensic samples.
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Affiliation(s)
- Seiji Kubo
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan; Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan.
| | - Keito Amai
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Jin Tanaka
- Forensic Science Laboratory, Ishikawa Prefectural Police Headquarters, 1-1 Kuratsuki, Kanazawa 920-8553, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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3
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Yu D, Zhang J, Gao N, Huo Y, Li W, Wang T, Zhang X, Simayijiang H, Yan J. Rapid and visual detection of specific bacteria for saliva and vaginal fluid identification with the lateral flow dipstick strategy. Int J Legal Med 2023; 137:1853-1863. [PMID: 37358650 DOI: 10.1007/s00414-023-03051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
Identification of body fluids is critical for crime scene reconstruction, and a source of investigation source of investigative leads. In recent years, microbial DNA analysis using sequencing and quantitative real-time polymerase chain reaction have been used to identify body fluids. However, these techniques are time-consuming, expensive, and require complex workflows. In this study, a new method for simultaneous detection of Streptococcus salivarius and Lactobacillus crispatus using polymerase chain reaction (PCR) in combination with a lateral flow dipstick (LFD) was developed to identify saliva and vaginal fluid in forensic samples. LFD results can be observed with the naked eye within 3 min with a sensitivity of 0.001 ng/µL DNA. The PCR-LFD assay was successfully used to detect S. salivarius and L. crispatus in saliva and vaginal fluid respectively, and showed negative results in blood, semen, nasal fluid, and skin. Moreover, saliva and vaginal fluid were detectable even at an extremely high mixing ratio of sample DNA (1:999). Saliva and vaginal fluid were identified in various mock forensic samples. These results indicate that saliva and vaginal fluid can be effectively detected by identifying S. salivarius and L. crispatus, respectively. Furthermore, we have shown that DNA samples used to identify saliva and vaginal fluid can also provide a complete short tandem repeat (STR) profile when used as source material for forensic STR profiling. In summary, our results suggest that PCR-LFD is a promising assay for rapid, simple, reliable, and efficient identification of body fluids.
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Affiliation(s)
- Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Wanting Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China.
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China.
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4
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Chierto E, Alessandrini F, Bini C, Carnevali E, Fabbri M, Fattorini P, Grignani P, Scarnicci F, Tozzo P, Verzeletti A, Pelotti S, Buscemi L, Robino C. An mRNA Profiling Study of Vaginal Swabs from Pre- and Postmenopausal Women. Curr Issues Mol Biol 2023; 45:6526-6537. [PMID: 37623230 PMCID: PMC10453267 DOI: 10.3390/cimb45080411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Body fluid identification by means of mRNA profiling provides valuable supplementary information in forensic investigations. In particular, the detection of vaginal mucosa mRNA markers is highly relevant in sexual assault cases. Although the vagina undergoes characteristic age-related physiological changes over a lifetime, few studies have evaluated the efficacy of vaginal mRNA markers in women of different ages. In this multicentric study, a 19-plex mRNA profiling assay including vaginal-specific markers (CYP2B7P1, MUC4, MYOZ1) was tested in a collection of 6-20-month-old vaginal swabs obtained from pre- (n = 84) and postmenopausal (n = 55) female volunteer donors. Overall, participating laboratories were able to correctly identify ~85% of samples as vaginal mucosa by mRNA profiling. The assay's success rate did not differ between the two age groups and was not affected by the time interval between swab collection and RNA analysis. MYOZ1 resulted a less sensitive vaginal marker compared to MUC4 and CYP2B7P1. A significant relative increase in the contribution to the total amplification signal was observed for MUC4, compared to CYP2B7P1 and MYOZ1, in postmenopausal women. Observation of other body fluids and tissues different from vaginal mucosa was also evaluated in connection to information on previous sexual activity and menstrual cycle phase at the time of sampling.
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Affiliation(s)
- Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy;
| | - Federica Alessandrini
- Section of Legal Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60126 Ancona, Italy
| | - Carla Bini
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, 40126 Bologna, Italy
| | - Eugenia Carnevali
- Unità Operativa Semplice Laboratory of Forensic Science, Section of Legal Medicine, Department of Medicine and Surgery, S. Maria Hospital, University of Perugia, 05100 Terni, Italy
| | - Matteo Fabbri
- Section of Legal Medicine, Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, 34129 Trieste, Italy
| | - Pierangela Grignani
- Section of Legal Medicine and Forensic Sciences, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Francesca Scarnicci
- Section of Legal Medicine, Department of Health Surveillance and Bioethics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Pamela Tozzo
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Forensic Medicine Unit, University of Brescia, 25123 Brescia, Italy
| | - Susi Pelotti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, 40126 Bologna, Italy
| | - Loredana Buscemi
- AOU Ospedali Riuniti Ancona, Polytechnic University of Marche, 60126 Ancona, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, 10126 Turin, Italy;
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5
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Dawnay N, Sheppard K. From crime scene to courtroom: A review of the current bioanalytical evidence workflows used in rape and sexual assault investigations in the United Kingdom. Sci Justice 2023; 63:206-228. [PMID: 36870701 DOI: 10.1016/j.scijus.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023]
Abstract
Sexual assault casework requires the collaboration of multiple agency staff to formalise an investigative pipeline running from crime scene to court. While the same could be said of many other forensic investigations, few require the additional support of health care staff and the combined forensic involvement of body-fluid examiners, DNA experts and analytical chemists. The sheer amount of collaborative effort between agencies is laid out through a detailed examination of the investigative workflow from crime scene to courtroom with each step in the pipelines detailed and discussed. Beginning with a review of sexual assault legislation in the United Kingdom this article details how sexual assault investigations are initiated by police and supported by sexual assault referral centre (SARC) staff who are often the first responders providing primary healthcare and patient support to victims while simultaneously collecting and assessing forensic evidence. Detailing the myriad of evidential material that can be documented and collected at the SARC, the review identifies and categorises key forensic tests to first detect and identify body-fluids recovered from evidence through to the secondary analysis of DNA to help identify the suspect. This review also focusses on the collection and analysis of biological material used to support the allegation that the sexual activity was non-consensual and provides a breakdown of common marks and trauma as well as a review of common analytical methods used to infer Drug Facilitated Sexual Assault (DFSA). The culmination of the investigative pipeline is discussed by reviewing the Rape and Serious Sexual Assault (RASSO) workflow used by the Crown Prosecution Service before providing our thoughts on the future of forensic analysis and possible changes to the described workflows.
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Affiliation(s)
- Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom.
| | - Kayleigh Sheppard
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, United Kingdom
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6
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Layne TR, Nouwairi RL, Fleming R, Blair H, Landers JP. Rapid Microchip Electrophoretic Separation of Novel Transcriptomic Body Fluid Markers for Forensic Fluid Profiling. MICROMACHINES 2022; 13:1657. [PMID: 36296010 PMCID: PMC9609788 DOI: 10.3390/mi13101657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Initial screening of criminal evidence often involves serological testing of stains of unknown composition and/or origin discovered at a crime scene to determine the tissue of origin. This testing is presumptive but critical for contextualizing the scene. Here, we describe a microfluidic approach for body fluid profiling via fluorescent electrophoretic separation of a published mRNA panel that provides unparalleled specificity and sensitivity. This centrifugal microfluidic approach expedites and automates the electrophoresis process by allowing for simple, rotationally driven flow and polymer loading through a 5 cm separation channel; with each disc containing three identical domains, multi-sample analysis is possible with a single disc and multi-sample detection per disc. The centrifugal platform enables a series of sequential unit operations (metering, mixing, aliquoting, heating, storage) to execute automated electrophoretic separation. Results show on-disc fluorescent detection and sizing of amplicons to perform comparably with a commercial 'gold standard' benchtop instrument and permitted sensitive, empirical discrimination between five distinct body fluids in less than 10 min. Notably, our microfluidic platform represents a faster, simpler method for separation of a transcriptomic panel to be used for forensically relevant body fluid identification.
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Affiliation(s)
- Tiffany R. Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - Renna L. Nouwairi
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - Rachel Fleming
- Institute of Environmental Science and Research Limited, Auckland 1025, New Zealand
| | - Haley Blair
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
| | - James P. Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22939, USA
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7
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Johannessen H, Gill P, Shanthan G, Fonneløp AE. Transfer, persistence and recovery of DNA and mRNA vaginal mucosa markers after intimate and social contact with Bayesian network analysis for activity level reporting. Forensic Sci Int Genet 2022; 60:102750. [PMID: 35914368 DOI: 10.1016/j.fsigen.2022.102750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/25/2023]
Abstract
In sexual assault cases, it can be challenging to identify the type of body fluids/ cell types present in a crime scene sample, especially the origin of epithelial cells. Therefore, more labs are applying mRNA body fluid analysis for saliva, skin and vaginal mucosa markers. To address activity level propositions, it is necessary to assign probabilities of transfer, persistence, prevalence and recovery of DNA and mRNA markers. In this study we analysed 158 samples (fingernail swabs, penile swabs and boxershorts) from 12 couples collected at different time points post intimate contact and after non-intimate contact in order to detect DNA from the person of interest (POI) and mRNA vaginal mucosa markers. Samples were DNA and RNA co-extracted and analysed with PowerPlex®Fusion 6C System and 19-plex mRNA primer mix respectively, using Endpoint PCR and the CE platform. Vaginal mucosa was detected up to 36 h post intimate contact, but also detected in one non-intimate contact sample. In 94% of intimate contact and 50 % of non-intimate contact samples the DNA results support the proposition that POI is the donor (LR ≥ 10,000). There was a strong association between the detection of vaginal mucosa and the average RFU value of the POI. The data were used to instantiate a comprehensive Bayesian network to evaluate the evidence at activity level, given alternate propositions conditioned upon indirect or direct transfer events. It is shown that the value of the evidence is mainly affected by the high DNA quantity (measured as mean RFU) that is recovered from the POI. The detection of vaginal mucosa had low impact upon the resultant likelihood ratio.
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Affiliation(s)
| | - Peter Gill
- Department of Forensic Medicine, University of Oslo, Norway; Department of Forensic Sciences, Oslo University Hospital, Norway
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8
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Identification of the vaginal secretion donor in mixture stains using polymorphic cSNPs on mRNA biomarkers. Forensic Sci Int Genet 2022; 59:102703. [DOI: 10.1016/j.fsigen.2022.102703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 01/27/2023]
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9
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Sijen T, Harbison S. On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime. Genes (Basel) 2021; 12:1728. [PMID: 34828334 PMCID: PMC8617621 DOI: 10.3390/genes12111728] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.
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Affiliation(s)
- Titia Sijen
- Division Human Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand;
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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10
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Tian H, Huang S, Bai P, Xiao X, Peng D, Zhao H, Liu Y, Feng Q, Liao M, Li F, Liang W. The effect of infertile semen on the mRNA-based body fluid identification. Electrophoresis 2021; 42:1614-1622. [PMID: 34233021 DOI: 10.1002/elps.202000238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 11/08/2022]
Abstract
In the past decade, mRNA markers have been well demonstrated as promising molecular markers in forensic body fluid identification (BFI), and successfully used in wide applications. Several studies have assessed the performance of semen-specific mRNA markers in distinguishing semen from other common body fluids at the crime scene. Infertility has been reported as a global health problem that is affecting approximately 15% of couples worldwide. Therefore, it is important for forensic researchers to consider the impact of infertility on semen identification. This study aimed to explore the effect of semen from infertile men (hereinafter "infertile semen") on BFI and to identify semen-specific mRNAs that can efficiently and accurately distinguish normal and infertile semen samples from other body fluids. Results showed that the selected five mRNAs (KLK3, TGM4, SEMG1, PRM1, and PRM2) performed a significantly high semen specificity in normal semen. Moreover, KLK3 was slightly influenced by infertile semen samples with over 98% positive results in all semen samples. The accuracy to predict normal semen reached up to 96.6% using the discrimination function Y1 with KLK3 and PRM1. However, when the infertile semen samples were included in discrimination function (function Y2 with KLK3), the accuracy rate of semen identification (including the normal and infertile semen) was down to 89.5%. Besides, the sensitivity of multiplex assay could reach down to 50pg. Our results suggest that it is important to consider the presence of infertile semen when using mRNAs to identify semen samples, which would have a far-reaching impact in forensic identification.
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Affiliation(s)
- Huan Tian
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Sicheng Huang
- Institute of Forensic Science, Chengdu Public Security Bureau, Chengdu, Sichuan, P. R. China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Xiao Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Duo Peng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Huan Zhao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuqing Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Qian Feng
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Fuping Li
- Human Sperm Bank, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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11
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Layne T, Jackson K, Scott A, Tanner NA, Piland A, Haverstick DM, Landers JP. Optimization of novel loop-mediated isothermal amplification with colorimetric image analysis for forensic body fluid identification. J Forensic Sci 2021; 66:1033-1041. [PMID: 33559876 DOI: 10.1111/1556-4029.14682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Accurate presumptive and confirmatory test use for forensic body fluid identification is essential for gaining contextual information for crime scene investigators. Loop-mediated isothermal amplification (LAMP) is an ideal method for forensic body fluid identification because it is highly specific and generates multi-sized amplicon DNA, and successful amplification results can be read out colorimetrically. Here, we show preliminary data on a LAMP method that rapidly identifies body fluids including venous blood, semen, and saliva, based on colorimetric response and image analysis. The method is designed for easy implementation into forensic casework protocols with minimal disruption to DNA analysis. LAMP naturally increases target specificity due to the use of multiple primers for one target and mRNA targets were used for tissue and human specificity. With colorimetric detection as an inherent part of LAMP, samples that are positive or negative for any of the body fluids are readily identified by image capture and analysis, thus eliminating subjectivity. Results show by using the 3D-printed imaging system specific color ranges can be set for easy determination of body fluids. The resulting color change can be seen in <30 min using a universal temperature and primer concentration for all body fluids. This simple method and imaging system allow for minimal hands-on time with objective image analysis and presents a pathway for creating a new potential method for forensic body fluid identification.
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Affiliation(s)
- Tiffany Layne
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Kimberly Jackson
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Anchi Scott
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | | | - Annie Piland
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Doris M Haverstick
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.,Departments of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, USA
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12
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Salzmann AP, Bamberg M, Courts C, Dørum G, Gosch A, Hadrys T, Hadzic G, Neis M, Schneider PM, Sijen T, den Berge MV, Wiegand P, Haas C. mRNA profiling of mock casework samples: Results of a FoRNAP collaborative exercise. Forensic Sci Int Genet 2020; 50:102409. [PMID: 33220528 DOI: 10.1016/j.fsigen.2020.102409] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/02/2020] [Accepted: 10/12/2020] [Indexed: 01/23/2023]
Abstract
In recent years, forensic mRNA profiling has increasingly been used to identify the origin of human body fluids. By now, several laboratories have implemented mRNA profiling and also use it in criminal casework. In 2018 the FoRNAP (Forensic RNA Profiling) group was established among a number of these laboratories with the aim of sharing experiences, discussing optimization potential, identifying challenges and suggesting solutions with regards to mRNA profiling and casework. To compare mRNA profiling methods and results a collaborative exercise was organized within the FoRNAP group. Seven laboratories from four countries received 16 stains, comprising six pure body fluid / tissue stains and ten mock casework samples. The laboratories were asked to analyze the provided stains with their in-house method (PCR/CE or MPS) and markers of choice. Five laboratories used a DNA/RNA co-extraction strategy. Overall, up to 11 mRNA markers per body fluid were analyzed. We found that mRNA profiling using different extraction and analysis methods as well as different multiplexes can be applied to casework-like samples. In general, high input samples were typed with high accuracy by all laboratories, regardless of the method used. Irrespective of the analysis strategy, samples of low input or mixed stains were more challenging to analyze and interpret since, alike to DNA profiling, a higher number of markers dropped out and/or additional unexpected markers not consistent with the cell type in question were detected. It could be shown that a plethora of different but valid analysis and interpretation strategies exist and are successfully applied in the Forensic Genetics community. Nevertheless, efforts aiming at optimizing and harmonizing interpretation approaches in order to achieve a higher consistency between laboratories might be desirable in the future. The simultaneous extraction of DNA alongside RNA showed to be an effective approach to identify not only the body fluid present but also to identify the donor(s) of the stain. This allows investigators to gain valuable information about the origin of crime scene samples and the course of events in a crime case.
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Affiliation(s)
| | - Malte Bamberg
- Institute of Legal Medicine, University Hospital, University of Ulm, Germany
| | - Cornelius Courts
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Annica Gosch
- Institute of Forensic Medicine, University Hospital of Schleswig-Holstein, Kiel, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, Munich, Germany
| | | | - Maximilian Neis
- Institute of Legal Medicine, Faculty of Medicine, University Hospital, University of Cologne, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, Faculty of Medicine, University Hospital, University of Cologne, Germany
| | - Titia Sijen
- Netherlands Forensic Institute, The Hague, the Netherlands
| | | | - Peter Wiegand
- Institute of Legal Medicine, University Hospital, University of Ulm, Germany
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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13
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Akutsu T, Watanabe K. A Proposed Procedure for Discriminating between Nasal Secretion and Saliva by RT-qPCR. Diagnostics (Basel) 2020; 10:diagnostics10080519. [PMID: 32722656 PMCID: PMC7460356 DOI: 10.3390/diagnostics10080519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 11/16/2022] Open
Abstract
In forensic casework, nasal secretion can be a good source of DNA. Moreover, saliva can prove useful in cases of sexual assault. However, discriminating between these body fluids is often difficult because of cross-reactivity between them on presumptive and confirmatory tests. Therefore, an RT-qPCR procedure was developed to discriminate between nasal secretion and saliva. Characteristic genes in nasal secretion and/or saliva (BPIFA1, STATH, HTN3, and PRH2) were selected as candidates. Discrimination criteria were established based on the expression levels of these markers in various body fluids. In addition, a flowchart was proposed and used to discriminate among nasal secretion, saliva, and other body fluids in various forensic samples. BPIFA1 was highly expressed in nasal secretion but was also expressed in saliva, semen, and vaginal fluid at trace levels. STATH was expressed in nasal secretion and saliva but not in other body fluids. HTN3 was specifically expressed in most of the saliva samples, as reported previously. Unexpectedly, PRH2 was expressed in only a few saliva samples. Using the proposed criteria and flowchart, nasal secretion and saliva were successfully discriminated among the various body fluids tested. The developed procedure could be useful in forensic casework.
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14
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Chirnside O, Lemalu A, Fleming R. Identification of nasal mucosa markers for forensic mRNA body fluid determination. Forensic Sci Int Genet 2020; 48:102317. [PMID: 32563047 DOI: 10.1016/j.fsigen.2020.102317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/10/2020] [Accepted: 05/26/2020] [Indexed: 01/26/2023]
Abstract
Biological fluids are commonly encountered as a form of evidence within forensic science, and can often provide important information relating to events which may have occurred. Over the years, significant advancements have been made with DNA profiling techniques, allowing for links to be made between an individual and cellular material recovered from a crime scene. While this DNA analysis can aid in linking an individual to a crime, it can often be beneficial to also determine the body fluid source of the DNA obtained from the sample in question for case context. One increasing area within the forensic field is the use of mRNA profiling for the identification of body fluids. The analysis of gene expression patterns can give information on cell function, and ultimately the body fluid source of the DNA in a sample. Over time this has led to the development of mRNA reverse transcriptase PCR assays to detect body fluid specific RNA transcripts for casework. During the use of these techniques nasal mucosa has been observed to give rise to false positive results. We report here on the identification of promising markers using RNA sequencing for the detection of nasal mucosa, with the aim to incorporate these markers into existing assays to assist in the identification of nasal mucosa and to assist in the interpretation of possible false positive results.
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Affiliation(s)
- Olivia Chirnside
- Forensic Science Program, Department of Chemistry, University of Auckland, New Zealand
| | - Anna Lemalu
- Institute of Environmental Science and Research Ltd (ESR), Mt Albert Science Centre, Hampstead Road, Private Bag, 92021, Auckland, New Zealand
| | - Rachel Fleming
- Institute of Environmental Science and Research Ltd (ESR), Mt Albert Science Centre, Hampstead Road, Private Bag, 92021, Auckland, New Zealand.
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15
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Liu B, Yang Q, Meng H, Shao C, Jiang J, Xu H, Sun K, Zhou Y, Yao Y, Zhou Z, Li H, Shen Y, Zhao Z, Tang Q, Xie J. Development of a multiplex system for the identification of forensically relevant body fluids. Forensic Sci Int Genet 2020; 47:102312. [PMID: 32480323 DOI: 10.1016/j.fsigen.2020.102312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 04/12/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
Abstract
Currently, mRNA profiling is widely investigated for forensic body fluid identification, while it is still required to advance the approach for those casework samples of limited quantity or low quality. The inclusion of circular RNAs (circRNAs) can facilitate the detection of mRNA markers in forensic body fluid identification. In this study, a multiplex assay for forensic body fluid identification (F18plex assay) was developed by incorporating 14 tissue-specific mRNA markers with circRNAs expression, 2 mRNA markers with high abundance and 2 housekeeping markers for the discrimination of the most common forensic body fluids, including blood, menstrual blood, saliva, vaginal secretion, semen and urine. The markers employed in the F18plex assay show similar specificity to previous reports. Additionally, even if all linear transcripts were completely erased, the expected markers in target biofluids could still be identified, which should help the discrimination of those aged biological stains. Results from sensitivity testing and the detection of mixtures demonstrate good sensitivity of the multiplex assay. Generally, full biomarker profiles could be obtained with ≥1 μl of blood, saliva, or semen, and ≥1 ng of total RNAs from menstrual blood, vaginal secretion, or urine samples, respectively, using this multiplex assay under the established conditions. Collectively, the newly established multiplex assay can assist in determining the biological origin of forensic stains.
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Affiliation(s)
- Baonian Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hang Meng
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jieqing Jiang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hongmei Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Kuan Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yuxiang Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Institute of Criminal Science and Technology, Shanghai Municipal Public Security Bureau, Shanghai, 200083, China
| | - Yiwen Shen
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ziqin Zhao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China; Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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16
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Akutsu T, Yokota I, Watanabe K, Sakurada K. Development of a multiplex RT-PCR assay and statistical evaluation of its use in forensic identification of vaginal fluid. Leg Med (Tokyo) 2020; 45:101715. [PMID: 32413723 DOI: 10.1016/j.legalmed.2020.101715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 01/09/2023]
Abstract
The identification of vaginal fluid from casework samples of sexual assaults provides important probative evidence of vaginal intercourse. The aim of this study was to establish a more specific procedure for identifying vaginal fluids for forensic purposes. Vaginal fluid marker candidates have been evaluated quantitatively and five of these markers (ESR1, SERPINB13, KLK13, CYP2B7P1, MUC4) have been amplified simultaneously by a multiplex reverse transcription-polymerase chain reaction (RT-PCR) procedure. Each amplicon has been separated and quantified automatically using chip electrophoresis. Subsequently, in the present study, detectability and cross-reactivity of the developed multiplex procedure were assessed in detail using various forensically relevant body fluids. Then, a cutoff value for the positive detection of vaginal fluids was set for each marker by Youden index. The ability of the multiplex RT-PCR assay to distinguish between vaginal and other body fluids was evaluated statistically using a likelihood ratio (LR) that was estimated using a Bayesian estimation approach to consider the infrequency of detection. A high LR was obtained when all five markers showed positive results (LR = 4.33 × 109; 95% credible interval, 3.95 × 107 -2.87 × 1012). The developed procedure was validated using vaginal fluid samples under various conditions. High LRs were found for aged vaginal fluid stains, although each amplicon peak was low. It was also able to identify vaginal stains mixed with other body fluids. In conclusion, the multiplex RT-PCR-based procedure followed by the statistical evaluation using LR could be a powerful tool for the objective identification of vaginal fluids.
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Affiliation(s)
- Tomoko Akutsu
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Isao Yokota
- Department of Biostatistics, Graduate School of Medicine, Hokkaido University, Nishi 15, Kita 7, Sapporo, Hokkaido 060-8638, Japan
| | - Ken Watanabe
- First Department of Forensic Science, National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Koichi Sakurada
- Department of Forensic Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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17
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Body fluid identification and assignment to donors using a targeted mRNA massively parallel sequencing approach – results of a second EUROFORGEN / EDNAP collaborative exercise. Forensic Sci Int Genet 2020; 45:102208. [DOI: 10.1016/j.fsigen.2019.102208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/30/2022]
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18
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Specific m(i)RNA profiling from DNA eluates for body fluid identification. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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A novel loop-mediated isothermal amplification method for identification of four body fluids with smartphone detection. Forensic Sci Int Genet 2019; 45:102195. [PMID: 31835180 DOI: 10.1016/j.fsigen.2019.102195] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/04/2019] [Accepted: 10/25/2019] [Indexed: 01/08/2023]
Abstract
Messenger RNA profiling for body fluid identification (bfID) is a useful approach to collect contextual information associated with a crime. Current methods require costly fluorescent probes, lengthy amplification protocols and/or time-consuming sample preparation. To simplify this process, we developed a bfID method that has the potential to be rapid in analysis time, inexpensive and fluorescence-free, combining a universal operating procedure with a high-throughout (microwell plate) platform for simultaneous detection of mRNA markers from whole blood, semen, saliva, and vaginal fluid. Full bfID sample preparation and analysis of 23 samples was completed in under 3 h using smart phone optical detection and analysis and show efficacy of the method in a validated blind study. The results provide an efficient, sensitive and specific approach to supplement the current biochemical tests in a forensic laboratory.
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20
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Watanabe K, Akutsu T. Evaluation of a co-extraction kit for mRNA, miRNA and DNA methylation-based body fluid identification. Leg Med (Tokyo) 2019; 42:101630. [PMID: 31751797 DOI: 10.1016/j.legalmed.2019.101630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 01/01/2023]
Abstract
Recently, messenger RNA (mRNA), micro RNA (miRNA), and DNA methylation (DNAm) have been reported as novel markers for body fluid identification (BFID). Comprehensive analysis of these markers should be a flexible and reliable BFID method for various types of forensic samples. However, independent extraction of all targets can be difficult depending on the usable amounts of samples. In this study, the applicability of a co-extraction kit for these molecules, the AllPrep DNA/RNA/miRNA Universal Kit (APU), was evaluated by comparing RNA and DNA extracted from blood and saliva stains by the APU with those extracted by standard kits for each molecule and by previously reported methods for mRNA/DNA or miRNA/DNA co-extraction. Electrophoresis using the Bioanalyzer platform and real-time PCR analysis revealed that the APU performed almost equivalently to each standard kit in the quality of RNA or DNA extracted and extraction efficiency of mRNAs, miRNAs, and DNA. Moreover, the APU outperformed the co-extraction methods, especially in RNA integrity and miRNA extraction efficiency. In addition, pyrosequencing revealed that the methylation ratios of DNA extracted by the APU were not different from those extracted by standard DNA extraction kits. Overall, the APU is applicable to comprehensive analysis of mRNA/miRNA/DNAm markers for BFID analysis. Because the DNA eluate can also be used for DNA typing, the APU may be among the best choices for forensic examination of body fluid samples in terms of its flexibility and reliability in BFID and efficiency in sample consumption.
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Affiliation(s)
- Ken Watanabe
- National Research Institute of Police Science, Chiba 277-0882, Japan.
| | - Tomoko Akutsu
- National Research Institute of Police Science, Chiba 277-0882, Japan
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21
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Salzmann AP, Russo G, Aluri S, Haas C. Transcription and microbial profiling of body fluids using a massively parallel sequencing approach. Forensic Sci Int Genet 2019; 43:102149. [DOI: 10.1016/j.fsigen.2019.102149] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022]
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22
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Ohta J, Sakurada K. Oral gram-positive bacterial DNA-based identification of saliva from highly degraded samples. Forensic Sci Int Genet 2019; 42:103-112. [DOI: 10.1016/j.fsigen.2019.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/17/2019] [Accepted: 06/22/2019] [Indexed: 12/29/2022]
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23
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Sharma S, Chophi R, Singh R. Forensic discrimination of menstrual blood and peripheral blood using attenuated total reflectance (ATR)-Fourier transform infrared (FT-IR) spectroscopy and chemometrics. Int J Legal Med 2019; 134:63-77. [PMID: 31388794 DOI: 10.1007/s00414-019-02134-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/26/2019] [Indexed: 02/07/2023]
Abstract
Body fluids are one of the most important pieces of evidence encountered in forensic cases especially in cases of sexual assault. Analysis of such evidence can help to establish a link between the perpetrator, the victim, and the crime scene and thereby assist in crime reconstruction. However, one of the biggest challenges faced by the investigators in sexual assault cases is that of ascertaining the issue of consent of the victim. In this matter, differentiation of menstrual blood (either in dried or stained form) from traumatic peripheral blood can give a potential solution on this particular aspect. A number of studies have been attempted to differentiate these two body fluids using various biochemical and serological methods. However, the methods employed are limited by factors such as sample destructivity and non-specificity, and the methods are susceptible to false positive results. In the present study, the scope of attenuated total reflectance (ATR)-Fourier transform infrared (FT-IR) spectroscopy in discriminating samples of menstrual blood and peripheral blood has been investigated, in combination with chemometric tools such as principal component analysis (PCA), partial least square regression (PLSR), and linear discriminant analysis (LDA). PCA resulted in 93.3% accuracy, whereas PLSR and LDA resulted in 100% accuracy for the discrimination of peripheral blood from menstrual blood. Application of PCA for the discrimination of menstrual blood from vaginal fluid and seminal fluid delivered 100% classification. Similarly, 100% classification was achieved while differentiating between menstrual blood and blood look-alike substances. Furthermore, in the current study, the effect of substrates on the analysis of menstrual blood has also been studied and described. Graphical Abstract.
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Affiliation(s)
- Sweety Sharma
- Department of Forensic Science, Punjabi University, Patiala, Punjab, 147002, India
| | - Rito Chophi
- Department of Forensic Science, Punjabi University, Patiala, Punjab, 147002, India
| | - Rajinder Singh
- Department of Forensic Science, Punjabi University, Patiala, Punjab, 147002, India.
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The potential use of Piwi-interacting RNA biomarkers in forensic body fluid identification: A proof-of-principle study. Forensic Sci Int Genet 2019; 39:129-135. [DOI: 10.1016/j.fsigen.2019.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/14/2018] [Accepted: 01/07/2019] [Indexed: 12/21/2022]
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25
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A method to estimate the age of bloodstains using quantitative PCR. Forensic Sci Int Genet 2019; 39:103-108. [DOI: 10.1016/j.fsigen.2018.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/10/2018] [Accepted: 12/13/2018] [Indexed: 01/03/2023]
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26
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Characterization of tissue-specific biomarkers with the expression of circRNAs in forensically relevant body fluids. Int J Legal Med 2019; 133:1321-1331. [PMID: 30810820 DOI: 10.1007/s00414-019-02027-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Messenger RNA (mRNA) markers have been extensively investigated for the identification of forensically relevant body fluids and tissues based on their expression profiles among cell types. As products of the backsplicing of pre-mRNAs, circular RNAs (circRNAs) share exonic sequences with their linear counterparts. The inclusion of circRNAs in mRNA profiling is shown to facilitate the detection of biomarkers in the identification of body fluids. In this study, we identified the expression of circRNAs of 14 out of 45 biomarkers from five body fluid types using outward-facing primer sets and revealed the ratio of circular to total transcripts of biomarkers by RNase R treatment. Furthermore, our results of qPCR analysis show that the inclusion of circRNAs in the detection of biomarkers, including HBA and ALAS2 for blood; MMP7 and MMP10 for menstrual blood; HTN3 for saliva; SPINK5, SERPINB3, ESR1, and CYP2B7P1 for vaginal secretions; TGM4, KLK3, and PRM2 for semen; and SLC22A6 and MIOX for urine, does not impair the specificity of these biomarkers. Additionally, a high copy number of targets from linear transcripts could be employed to increase the detection sensitivity of TGM4 and KLK3 with a low expression level of circRNAs in urine samples. Altogether, these results will help with the development of robust multiplex assays for body fluid identification.
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27
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Bhowmick SS, Bhattacharjee D, Rato L. Identification of tissue-specific tumor biomarker using different optimization algorithms. Genes Genomics 2018; 41:431-443. [PMID: 30535858 DOI: 10.1007/s13258-018-0773-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 12/03/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND Identification of differentially expressed genes, i.e., genes whose transcript abundance level differs across different biological or physiological conditions, was indeed a challenging task. However, the inception of transcriptome sequencing (RNA-seq) technology revolutionized the simultaneous measurement of the transcript abundance levels for thousands of genes. OBJECTIVE In this paper, such next-generation sequencing (NGS) data is used to identify biomarker signatures for several of the most common cancer types (bladder, colon, kidney, brain, liver, lung, prostate, skin, and thyroid) METHODS: Here, the problem is mapped into the comparison of optimization algorithms for selecting a set of genes that lead to the highest classification accuracy of a two-class classification task between healthy and tumor samples. As the optimization algorithms Artificial Bee Colony (ABC), Ant Colony Optimization, Differential Evolution, and Particle Swarm Optimization are chosen for this experiment. A standard statistical method called DESeq2 is used to select differentially expressed genes before being feed to the optimization algorithms. Classification of healthy and tumor samples is done by support vector machine RESULTS: Cancer-specific validation yields remarkably good results in terms of accuracy. Highest classification accuracy is achieved by the ABC algorithm for Brain lower grade glioma data is 99.10%. This validation is well supported by a statistical test, gene ontology enrichment analysis, and KEGG pathway enrichment analysis for each cancer biomarker signature CONCLUSION: The current study identified robust genes as biomarker signatures and these identified biomarkers might be helpful to accurately identify tumors of unknown origin.
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Affiliation(s)
- Shib Sankar Bhowmick
- Department of Electronics and Communication Engineering, Heritage Institute of Technology, Kolkata, 700107, India.
| | - Debotosh Bhattacharjee
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, 700032, India
| | - Luis Rato
- Department of Informatics, University of Evora, 7004-516, Evora, Portugal
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28
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Tsai LC, Su CW, Lee JCI, Lu YS, Chen HC, Lin YC, Linacre A, Hsieh HM. The detection and identification of saliva in forensic samples by RT-LAMP. Forensic Sci Med Pathol 2018; 14:469-477. [PMID: 30058014 DOI: 10.1007/s12024-018-0008-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
We report on a novel method for saliva identification by reverse transcription-loop-mediated isothermal amplification (RT-LAMP). In our previous report, real-time RT-LAMP was used for blood identification by using HBB detection as a model but in this advanced study, this method was refined for the identification of the more challenging body fluid of saliva. Expression of the18S rRNA gene was used as the internal control and the Statherin (STATH) gene as the saliva-specific marker. A turbidimeter was used for real-time detection of the RT-LAMP products, and confirmation was obtained that the real products were generated using: agarose gel electrophoresis, calcein fluorescence detection and/or enzymatic digestion. The specificity of the test was performed using 42 samples including 7 different body fluids, and the expression of STATH was only observed in all the saliva samples (6) with a threshold time of 39.4 ± 2.9 min. Sensitivity testing showed that RT-LAMP products for STATH were stably detected when the RNA template was not less than 6.25 ng. When the primer concentrations for STATH were two times that of 18S rRNA, saliva could be identified in the body fluid mixtures even at a ratio (saliva:semen) of 1:3 (without loop primer)/1:5 (with loop primer). A multiplex RT-LAMP was established to simultaneously amplify the 18S rRNA and STATH genes, and applied to the identification of saliva on ten non-probative cigarette butts. A positive result for saliva was obtained from all ten butts, even for those that returned a negative or ambiguous result using the amylase test. A direct RT-LAMP test is also reported where the RNA extraction step was omitted to speed the collection of data and all tests using either the simplex or multiplex RT-LAMP resulted in a positive response if saliva was present. Our data provide a simple and effective means to detect the presence of saliva.
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Affiliation(s)
- Li-Chin Tsai
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan, Republic of China
| | - Chih-Wen Su
- Forensic Biology Division, Criminal Investigation Bureau, National Police Administration, No.5 Lane 553, Sec. 4, Zhongxiao E. RD., Xinyi District, Taipei, 11072, Taiwan, Republic of China
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No. 1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan, Republic of China
| | - Yu-Sheng Lu
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan, Republic of China
| | - Hsuan-Chen Chen
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan, Republic of China
| | - Yu-Chih Lin
- Taichung City Government Police Department, 588 Wenxin Road Section 2, Xitun District, Taichung, 40758, Taiwan, Republic of China
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, 5001, Australia
| | - Hsing-Mei Hsieh
- Department of Forensic Science, Central Police University, 56 Shu-Jen Road, Kwei-San, Taoyuan, 33304, Taiwan, Republic of China.
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Ingold S, Dørum G, Hanson E, Berti A, Branicki W, Brito P, Elsmore P, Gettings K, Giangasparo F, Gross T, Hansen S, Hanssen E, Kampmann ML, Kayser M, Laurent FX, Morling N, Mosquera-Miguel A, Parson W, Phillips C, Porto M, Pośpiech E, Roeder A, Schneider P, Schulze Johann K, Steffen C, Syndercombe-Court D, Trautmann M, van den Berge M, van der Gaag K, Vannier J, Verdoliva V, Vidaki A, Xavier C, Ballantyne J, Haas C. Body fluid identification using a targeted mRNA massively parallel sequencing approach – results of a EUROFORGEN/EDNAP collaborative exercise. Forensic Sci Int Genet 2018; 34:105-115. [DOI: 10.1016/j.fsigen.2018.01.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/17/2017] [Accepted: 01/05/2018] [Indexed: 11/30/2022]
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Satoh T, Kouroki S, Ogawa K, Tanaka Y, Matsumura K, Iwase S. Development of mRNA-based body fluid identification using reverse transcription loop-mediated isothermal amplification. Anal Bioanal Chem 2018; 410:4371-4378. [PMID: 29696299 DOI: 10.1007/s00216-018-1088-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 11/24/2022]
Abstract
Identifying body fluids from forensic samples can provide valuable evidence for criminal investigations. Messenger RNA (mRNA)-based body fluid identification was recently developed, and highly sensitive parallel identification using reverse transcription polymerase chain reaction (RT-PCR) has been described. In this study, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a simple, rapid assay for identifying three common forensic body fluids, namely blood, semen, and saliva, and evaluated its specificity and sensitivity. Hemoglobin beta (HBB), transglutaminase 4 (TGM4), and statherin (STATH) were selected as marker genes for blood, semen, and saliva, respectively. RT-LAMP could be performed in a single step including both reverse transcription and DNA amplification under an isothermal condition within 60 min, and detection could be conveniently performed via visual fluorescence. Marker-specific amplification was performed in each assay, and no cross-reaction was observed among five representative forensically relevant body fluids. The detection limits of the assays were 0.3 nL, 30 nL, and 0.3 μL for blood, semen, and saliva, respectively, and their sensitivities were comparable with those of RT-PCR. Furthermore, RT-LAMP assays were applicable to forensic casework samples. It is considered that RT-LAMP is useful for body fluid identification.
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Affiliation(s)
- Tetsuya Satoh
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan.
| | - Seiya Kouroki
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Keita Ogawa
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Yorika Tanaka
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Kazutoshi Matsumura
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
| | - Susumu Iwase
- Forensic Science Laboratory, Kumamoto Prefectural Police Headquarters, 6-18-1 Suizenji, Chuo-ku Kumamoto-shi, Kumamoto, 862-8610, Japan
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Lee JW, Jung JY, Lim SK. Simple and rapid identification of saliva by detection of oral streptococci using direct polymerase chain reaction combined with an immunochromatographic strip. Forensic Sci Int Genet 2018; 33:155-160. [DOI: 10.1016/j.fsigen.2017.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/14/2017] [Accepted: 12/19/2017] [Indexed: 01/25/2023]
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32
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Stafford-Allen B, Dawnay N, Hanson EK, Ball G, Gupta A, Blackman S, French DJ, Duxbury N, Ballantyne J, Wells S. Development of HyBeacon ® probes for specific mRNA detection using body fluids as a model system. Mol Cell Probes 2017; 38:51-59. [PMID: 29175285 DOI: 10.1016/j.mcp.2017.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022]
Abstract
HyBeacons are linear oligonucleotides which incorporate fluorescent dyes covalently linked to internal nucleotides. They have previously been used with PCR and isothermal amplification to interrogate SNPs and STRs in fields as diverse as clinical diagnostics, food authentication, and forensic DNA profiling. This work explores their use for the identification of expressed gene sequences through mRNA profiling. The use of mRNA is becoming increasingly common in forensic casework to identify body fluids on evidence items, as it offers higher specificity and fewer false positives than current chemical presumptive testing methods. The work presented here details the development of a single-step one-tube RT-PCR assay to detect the presence of body fluids of forensic interest (saliva, blood, seminal fluid, vaginal fluid and menstrual blood) using HyBeacon® probes and melt curve analysis. Each assay shows a high degree of specificity to the target body fluid mRNA suggesting there is no requirement to remove genomic DNA prior to analysis. Of the five assays developed, four were able to detect between 10 and 100 copies of target cDNA, the fifth 1000 copies of target. The results presented here demonstrate that such an approach can be optimised for non-expert users and further areas of work are discussed.
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Affiliation(s)
- Beccy Stafford-Allen
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK.
| | - Nick Dawnay
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Erin K Hanson
- National Center for Forensic Science, PO Box 162367, Orlando, FL, 32816-2367, USA
| | - Glyn Ball
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - Ambika Gupta
- Department of Pharmacy and Forensic Science, King's College London, Faculty of Life Sciences and Medicine, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK
| | - Stephen Blackman
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - David J French
- Product Development Group, LGC Ltd, Queens Road, Teddington, TW11 0LY, UK
| | - Nicola Duxbury
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
| | - Jack Ballantyne
- National Center for Forensic Science, PO Box 162367, Orlando, FL, 32816-2367, USA; Department of Chemistry, University of Central Florida, PO Box 162366, Orlando, FL, 32816-2366, USA
| | - Simon Wells
- Product Development Group, LGC Ltd, Culham Science Centre, Abingdon, OX14 3ED, UK
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Hanson E, Ballantyne J. Human Organ Tissue Identification by Targeted RNA Deep Sequencing to Aid the Investigation of Traumatic Injury. Genes (Basel) 2017; 8:genes8110319. [PMID: 29125589 PMCID: PMC5704232 DOI: 10.3390/genes8110319] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 11/16/2022] Open
Abstract
Molecular analysis of the RNA transcriptome from a putative tissue fragment should permit the assignment of its source to a specific organ, since each will exhibit a unique pattern of gene expression. Determination of the organ source of tissues from crime scenes may aid in shootings and other investigations. We have developed a prototype massively parallel sequencing (MPS) mRNA profiling assay for organ tissue identification that is designed to definitively identify 10 organ/tissue types using a targeted panel of 46 mRNA biomarkers. The identifiable organs and tissues include brain, lung, liver, heart, kidney, intestine, stomach, skeletal muscle, adipose, and trachea. The biomarkers were chosen after iterative specificity testing of numerous candidate genes in various tissue types. The assay is very specific, with little cross-reactivity with non-targeted tissue, and can detect RNA mixtures from different tissues. We also demonstrate the ability of the assay to successful identify the tissue source of origin using a single blind study.
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Affiliation(s)
- Erin Hanson
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32816, USA.
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32816, USA.
- Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
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34
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Holtkötter H, Schwender K, Wiegand P, Peiffer H, Vennemann M. Improving body fluid identification in forensic trace evidence—construction of an immunochromatographic test array to rapidly detect up to five body fluids simultaneously. Int J Legal Med 2017; 132:83-90. [DOI: 10.1007/s00414-017-1724-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
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Abstract
In forensic investigations, the identification of the cellular or body fluid source of biological evidence can provide crucial probative information for the court. Messenger RNA (mRNA) profiling has become a valuable tool for body fluid and cell type identification due to its high sensitivity and compatibility with DNA analysis. However, using a single marker to determine the somatic origin of a sample can lead to misinterpretation as a result of cross-reactions. While false positives may be avoided through the simultaneous detection of multiple markers per body fluid, this approach is currently limited by the small number of known differentially expressed mRNAs. Here we characterise six novel mRNAs, partly identified from RNA-Seq, which can supplement existing markers for the detection of circulatory blood, semen (with and without spermatozoa), and menstrual fluid: HBD and SLC4A1 for blood, TNP1 for spermatozoa, KLK2 for seminal fluid, and MMP3 and STC1 for menstrual fluid. Respective expression profiles were evaluated by singleplex endpoint reverse transcription polymerase chain reaction (RT-PCR). HBD, SLC4A1, and KLK2 were specific to their target body fluids. TNP1, MMP3, and STC1 each cross-reacted with two non-target samples; however, these signals were below 350RFU, not reproducible, and likely resulted from large body fluid inputs. All candidates were more sensitive for the detection of their target body fluids than corresponding well-known mRNAs, in particular those for menstrual fluid. The increased sensitivities were statistically significant, except for KLK2. Thus, the new mRNAs introduced here are promising new targets for improved body fluid profiling.
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Affiliation(s)
- Patricia P Albani
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand; The Institute of Environmental Science and Research Ltd. (ESR), Auckland, New Zealand
| | - Rachel Fleming
- The Institute of Environmental Science and Research Ltd. (ESR), Auckland, New Zealand.
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36
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Evaluation of the inclusion of circular RNAs in mRNA profiling in forensic body fluid identification. Int J Legal Med 2017; 132:43-52. [PMID: 28948359 DOI: 10.1007/s00414-017-1690-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/12/2017] [Indexed: 01/16/2023]
Abstract
The use of messenger RNA (mRNA) profiling is considered a promising method in the identification of forensically relevant body fluids which can provide crucial information for reconstructing a potential crime. However, casework samples are usually of limited quantity or have been subjected to degradation, which requires improvement of body fluid identification. Circular RNAs (circRNAs), a class of products from the backsplicing of pre-mRNAs, are shown to have high abundance, remarkable stability, and cell type-specific expression in human cells. In this study, we investigated whether the inclusion of circRNAs in mRNA profiling improve the detection of biomarkers including δ-aminolevulinate synthase 2 (ALAS2) and matrix metallopeptidase 7 (MMP7) in body fluid identification. The major circRNAs of ALAS2 and MMP7 were first identified and primer sets for the simultaneous detection of linear and circular transcripts were developed. The inclusion of circRNAs in mRNA profiling showed improved detection sensitivity and stability of biomarkers revealed by using serial dilutions, mixed samples, and menstrual bloodstains as well as degraded and aged samples. Therefore, the inclusion of circRNAs in mRNA profiling should facilitate the detection of mRNA markers in forensic body fluid identification.
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37
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Antunes J, Silva DS, Balamurugan K, Duncan G, Alho CS, McCord B. Forensic discrimination of vaginal epithelia by DNA methylation analysis through pyrosequencing. Electrophoresis 2016; 37:2751-2758. [DOI: 10.1002/elps.201600037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Joana Antunes
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Deborah S.B.S. Silva
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
- Faculty of Biosciences; Laboratory of Human and Molecular Genetics; PUCRS; Porto Alegre Brazil
| | | | - George Duncan
- DNA Laboratory; Broward County Sheriff's Office; Fort Lauderdale FL USA
| | - Clarice S. Alho
- Faculty of Biosciences; Laboratory of Human and Molecular Genetics; PUCRS; Porto Alegre Brazil
| | - Bruce McCord
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
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38
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Affiliation(s)
- Rachel K Harstad
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Alexander C Johnson
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Megan M Weisenberger
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Michael T Bowser
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
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39
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Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers. Forensic Sci Int Genet 2015; 18:21-32. [DOI: 10.1016/j.fsigen.2014.11.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
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40
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Song F, Luo H, Hou Y. Developed and evaluated a multiplex mRNA profiling system for body fluid identification in Chinese Han population. J Forensic Leg Med 2015; 35:73-80. [PMID: 26311108 DOI: 10.1016/j.jflm.2015.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/28/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
In forensic casework, identification the cellular origin from a biological sample is crucial to the case investigation and reconstruction in crime scene. DNA/RNA co-extraction for STR typing and human body fluids identification has been proposed as an efficient and comprehensive assay for forensic analysis. Several cell-specific messenger RNA (mRNA) markers for identification of the body fluids have been proposed by previous studies. In this study, a novel multiplex mRNA profiling system included 19 markers was developed and performed by reverse transcription endpoint polymerase chain reaction (RT-PCR). The multiplex combined 3 housekeeping gene markers and 16 cell-specific markers that have been used to identify five types of human body fluids: peripheral blood, semen, saliva, vaginal secretions and menstrual blood. The specificity, sensitivity, stability and detectability of the mixture were explored in our study. Majority of the cell-specific mRNA markers showed high specificity, although cross-reactivity was observed sporadically. Specific profiling for per body fluid was obtained. Moreover, the interpretation guidelines for inference of body fluid types were performed according to the A. Lindenbergh et al. The scoring guidelines can be applied to any RNA multiplex, which was based on six different scoring categories (observed, observed and fits, sporadically observed and fits, not observed, sporadically observed, not reliable, and non-specific due to high input). The simultaneous extraction of DNA showed positive full or partial profiling results of all samples. It demonstrated that the approach of combined STR-profiling and RNA profiling was suitable and reliable to detect the donor and origin of human body fluids in Chinese Han population.
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Affiliation(s)
- Feng Song
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Science and Forensic Medicine, Sichuan University (West China University of Medical Sciences), Chengdu 610041, Sichuan, China.
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41
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Park HY, Son BN, Seo YI, Lim SK. Comparison of Four Saliva Detection Methods to Identify Expectorated Blood Spatter. J Forensic Sci 2015. [DOI: 10.1111/1556-4029.12864] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hee-Yeon Park
- DNA Analysis Section; Busan Institute of National Forensic Service; Gyeongsangnam-do 626-742 South Korea
| | - Bu-Nam Son
- Scientific Investigation Center; Gyongnam Provincial Police Agency; Gyeongsangnam-do 641-797 South Korea
| | - Young-Il Seo
- Forensic Safety Division; National Forensic Service; Gangwon-do 220-170 South Korea
| | - Si-Keun Lim
- Forensic DNA Division; National Forensic Service; Gangwon-do 220-170 South Korea
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42
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Breathnach M, Moore E. Background Levels of Salivary-α-amylase Plus Foreign DNA in Cases of Oral Intercourse: a Female Perspective. J Forensic Sci 2015. [DOI: 10.1111/1556-4029.12866] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michelle Breathnach
- Department of Applied Science; Limerick Institute of Technology; Limerick Ireland
| | - Elizabeth Moore
- Department of Applied Science; Limerick Institute of Technology; Limerick Ireland
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43
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Haas C, Hanson E, Banemann R, Bento A, Berti A, Carracedo Á, Courts C, Cock GD, Drobnic K, Fleming R, Franchi C, Gomes I, Hadzic G, Harbison S, Hjort B, Hollard C, Hoff-Olsen P, Keyser C, Kondili A, Maroñas O, McCallum N, Miniati P, Morling N, Niederstätter H, Noël F, Parson W, Porto M, Roeder A, Sauer E, Schneider P, Shanthan G, Sijen T, Syndercombe Court D, Turanská M, van den Berge M, Vennemann M, Vidaki A, Zatkalíková L, Ballantyne J. RNA/DNA co-analysis from human skin and contact traces – results of a sixth collaborative EDNAP exercise. Forensic Sci Int Genet 2015; 16:139-147. [DOI: 10.1016/j.fsigen.2015.01.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/12/2014] [Accepted: 01/04/2015] [Indexed: 11/25/2022]
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44
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Farash K, Hanson EK, Ballantyne J. Enhanced genetic analysis of single human bioparticles recovered by simplified micromanipulation from forensic 'touch DNA' evidence. J Vis Exp 2015:52612. [PMID: 25867046 PMCID: PMC4401234 DOI: 10.3791/52612] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
DNA profiles can be obtained from 'touch DNA' evidence, which comprises microscopic traces of human biological material. Current methods for the recovery of trace DNA employ cotton swabs or adhesive tape to sample an area of interest. However, such a 'blind-swabbing' approach will co-sample cellular material from the different individuals, even if the individuals' cells are located in geographically distinct locations on the item. Thus, some of the DNA mixtures encountered in touch DNA samples are artificially created by the swabbing itself. In some instances, a victim's DNA may be found in significant excess thus masking any potential perpetrator's DNA. In order to circumvent the challenges with standard recovery and analysis methods, we have developed a lower cost, 'smart analysis' method that results in enhanced genetic analysis of touch DNA evidence. We describe an optimized and efficient micromanipulation recovery strategy for the collection of bio-particles present in touch DNA samples, as well as an enhanced amplification strategy involving a one-step 5 µl microvolume lysis/STR amplification to permit the recovery of STR profiles from the bio-particle donor(s). The use of individual or few (i.e., "clumps") bioparticles results in the ability to obtain single source profiles. These procedures represent alternative enhanced techniques for the isolation and analysis of single bioparticles from forensic touch DNA evidence. While not necessary in every forensic investigation, the method could be highly beneficial for the recovery of a single source perpetrator DNA profile in cases involving physical assault (e.g., strangulation) that may not be possible using standard analysis techniques. Additionally, the strategies developed here offer an opportunity to obtain genetic information at the single cell level from a variety of other non-forensic trace biological material.
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Affiliation(s)
- Katherine Farash
- Forensic Science Graduate Program, Biochemistry Track, University of Central Florida; Department of Chemistry, University of Central Florida
| | - Erin K Hanson
- National Center for Forensic Science, University of Central Florida
| | - Jack Ballantyne
- Forensic Science Graduate Program, Biochemistry Track, University of Central Florida; Department of Chemistry, University of Central Florida; National Center for Forensic Science, University of Central Florida;
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45
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Donfack J, Wiley A. Mass spectrometry-based cDNA profiling as a potential tool for human body fluid identification. Forensic Sci Int Genet 2015; 16:112-120. [PMID: 25594487 DOI: 10.1016/j.fsigen.2014.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
Abstract
Several mRNA markers have been exhaustively evaluated for the identification of human venous blood, saliva, and semen in forensic genetics. As new candidate human body fluid specific markers are discovered, evaluated, and reported in the scientific literature, there is an increasing trend toward determining the ideal markers for cDNA profiling of body fluids of forensic interest. However, it has not been determined which molecular genetics-based technique(s) should be utilized to assess the performance of these markers. In recent years, only a few confirmatory, mRNA/cDNA-based methods have been evaluated for applications in body fluid identification. The most frequently described methods tested to date include quantitative polymerase chain reaction (qPCR) and capillary electrophoresis (CE). However these methods, in particular qPCR, often favor narrow multiplex PCR due to the availability of a limited number of fluorescent dyes/tags. In an attempt to address this technological constraint, this study explored matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for human body fluid identification via cDNA profiling of venous blood, saliva, and semen. Using cDNA samples at 20pg input phosphoglycerate kinase 1 (PGK1) amounts, body fluid specific markers for the candidate genes were amplified in their corresponding body fluid (i.e., venous blood, saliva, or semen) and absent in the remaining two (100% specificity). The results of this study provide an initial indication that MALDI-TOF MS is a potential fluorescent dye-free alternative method for body fluid identification in forensic casework. However, the inherent issues of low amounts of mRNA, and the damage caused to mRNA by environmental exposures, extraction processes, and storage conditions are important factors that significantly hinder the implementation of cDNA profiling into forensic casework.
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Affiliation(s)
- Joseph Donfack
- Counterterrorism and Forensic Science Research Unit, Federal Bureau of Investigation Laboratory Division, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Anissa Wiley
- Counterterrorism and Forensic Science Research Unit, Visiting Scientist Program, Federal Bureau of Investigation Laboratory Division, Quantico, VA 22135, USA
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46
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Akutsu T, Kitayama T, Watanabe K, Sakurada K. Comparison of automated and manual purification of total RNA for mRNA-based identification of body fluids. Forensic Sci Int Genet 2015; 14:11-7. [DOI: 10.1016/j.fsigen.2014.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/10/2014] [Accepted: 09/08/2014] [Indexed: 01/21/2023]
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47
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Danaher P, White RL, Hanson EK, Ballantyne J. Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets. Forensic Sci Int Genet 2015; 14:18-30. [DOI: 10.1016/j.fsigen.2014.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/27/2014] [Accepted: 09/07/2014] [Indexed: 11/25/2022]
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48
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Hanson EK, Mirza M, Rekab K, Ballantyne J. The identification of menstrual blood in forensic samples by logistic regression modeling of miRNA expression. Electrophoresis 2014; 35:3087-95. [DOI: 10.1002/elps.201400171] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/04/2014] [Accepted: 08/12/2014] [Indexed: 11/10/2022]
Affiliation(s)
| | - Mohid Mirza
- Molecular Biology and Microbiology (Biomedical Sciences) Undergraduate Program; University of Central Florida; Orlando FL USA
| | - Kamel Rekab
- University of Missouri-Kansas City; Kansas City MO USA
| | - Jack Ballantyne
- National Center for Forensic Science; Orlando FL USA
- Department of Chemistry; University of Central Florida; Orlando FL USA
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49
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Schweighardt AJ, Tate CM, Scott KA, Harper KA, Robertson JM. Evaluation of Commercial Kits for Dual Extraction of DNA and RNA from Human Body Fluids,,. J Forensic Sci 2014; 60:157-65. [DOI: 10.1111/1556-4029.12586] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 11/30/2013] [Accepted: 12/21/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Andrew J. Schweighardt
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Courtney M. Tate
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Kristina A. Scott
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - Kathryn A. Harper
- Counterterrorism and Forensic Science Research Unit; Visiting Scientist Program; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
| | - James M. Robertson
- Counterterrorism and Forensic Science Research Unit; Federal Bureau of Investigation Laboratory Division; 2501 Investigation Parkway Quantico VA 22135
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Identification of body fluid-specific DNA methylation markers for use in forensic science. Forensic Sci Int Genet 2014; 13:147-53. [PMID: 25128690 DOI: 10.1016/j.fsigen.2014.07.011] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/04/2014] [Accepted: 07/19/2014] [Indexed: 12/31/2022]
Abstract
DNA methylation, which occurs at the 5'-position of the cytosine in CpG dinucleotides, has great potential for forensic identification of body fluids, because tissue-specific patterns of DNA methylation have been demonstrated, and DNA is less prone to degradation than proteins or RNA. Previous studies have reported several body fluid-specific DNA methylation markers, but DNA methylation differences are sometimes low in saliva and vaginal secretions. Moreover, specific DNA methylation markers in four types of body fluids (blood, saliva, semen, and vaginal secretions) have not been investigated with genome-wide profiling. Here, we investigated novel DNA methylation markers for identification of body fluids for use in forensic science using the Illumina HumanMethylation 450K bead array, which contains over 450,000 CpG sites. Using methylome data from 16 samples of blood, saliva, semen, and vaginal secretions, we first selected 2986 hypermethylated or hypomethylated regions that were specific for each type of body fluid. We then selected eight CpG sites as novel, forensically relevant DNA methylation markers: cg06379435 and cg08792630 for blood, cg26107890 and cg20691722 for saliva, cg23521140 and cg17610929 for semen, and cg01774894 and cg14991487 for vaginal secretions. These eight selected markers were evaluated in 80 body fluid samples using pyrosequencing, and all showed high sensitivity and specificity for identification of the target body fluid. We suggest that these eight DNA methylation markers may be good candidates for developing an effective molecular assay for identification of body fluids in forensic science.
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